GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gtsD in Magnetospirillum magneticum AMB-1

Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate WP_011385763.1 AMB_RS17210 molybdenum import ATP-binding protein ModC

Query= TCDB::Q88P35
         (384 letters)



>lcl|NCBI__GCF_000009985.1:WP_011385763.1 AMB_RS17210 molybdenum
           import ATP-binding protein ModC
          Length = 363

 Score =  146 bits (369), Expect = 8e-40
 Identities = 103/304 (33%), Positives = 160/304 (52%), Gaps = 31/304 (10%)

Query: 23  DIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGGAI------LIDEQDVSGMSPKD 76
           D++LS   G    L G SG GK++++N +AGL +   G+I      L D +    + P+ 
Sbjct: 16  DVRLSAGPG-VTALYGRSGSGKTSVINMVAGLSRPDEGSISVDGRVLFDSRSGIDLPPEA 74

Query: 77  RDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVAKLLQIEHLLARKPAQL 136
           R +  VFQ + L+P +SVR N+EFG K+  LP A   + + +V +LL IE LL R+PA+L
Sbjct: 75  RRLGYVFQEHRLFPHLSVRGNLEFGQKL--LPSAERTQSLDKVVELLGIESLLDRRPAKL 132

Query: 137 SGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHDQ 196
           SGG++QRVA+GRAL   P+I L DEPL+ LD   + E+   +  + +R     +YV+H  
Sbjct: 133 SGGEKQRVAIGRALLASPRILLMDEPLAALDPARKAEVLPFIAQLARRFSVPILYVSHSM 192

Query: 197 IEAMTLGDKVAVMKDGIIQQFGTPQQIYNDP----------ANQFVASFIGSPPMNFIPV 246
            E + L D +A+M  G +   G  + +  DP          A   + + + S    F   
Sbjct: 193 DEVLRLADTLALMDGGKVAASGPLESLMGDPGLRPLTGRYEAGAVIGAVVSSHDSGFGIS 252

Query: 247 RLARQDGRLLALLDSGQARCELPLG-EAADALEGREIILGIR-PEQIALGAADGNGLPAI 304
           RLA   G L+        R ELP+G +    +  R++ + I  P+++++     N LPAI
Sbjct: 253 RLAFDGGTLIV------GRSELPVGAKVRLRIHARDVAIAIEPPDRVSI----RNVLPAI 302

Query: 305 RAEV 308
              V
Sbjct: 303 VVSV 306


Lambda     K      H
   0.320    0.137    0.391 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 351
Number of extensions: 16
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 384
Length of database: 363
Length adjustment: 30
Effective length of query: 354
Effective length of database: 333
Effective search space:   117882
Effective search space used:   117882
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory